Shiloh: Camp video showing how to fill out a corps with 1 star units by swapping officers.
The original battle plan was to avoid triggering both VPs to get as much time as possible to wipe out and surround all of the enemy units in the initial phases. Then avoid triggering the landing VP with its very large radius until the last minute. Instead I lost track of time and ended up having to win on day2. Improvising on day 2 worked out pretty well and ended with a pretty good result.
Losses: 23706(6189 of own units) Kills: 53466﻿

Changing the unit modifier settings only affects the experience gain of units. This will result in your officers ranking up again sooner, but officers that end the battle under the modded xp caps will still get demoted if you are using old saves. The mod is designed to work by starting a new campaign so unfortunately there is no way to get around this when using old saves.

Shiloh will be up tomorrow. As the last several battles have been, it's a bit of a mess with the highlight of not paying attention and going to day 2. But the results turned out pretty good so can't complain.

Can you transfer one or both units to a different division to try and split them up? Or just get the duplicated unit into a slot you don't need? Worth trying moving the division to a different corps as well.
My initial impression is that this is unlikely to be due to the mod changes. This one has no unit duplication type changes, though even the Rebalance mod does that outside of camp. Based on what you've described it sounds like somehow a unique got duplicated but kept the same identifier. Though that only would explain some of the things you are seeing.
If you want to send me a save I can poke around a bit, but best case scenario maybe I can find a way to delete the duplicate.

I've never seen that in any mod or the base game. Does the unit have the same officer as the one it duplicated from? The same battle history?
Any other details you can provide like what happened to the original unit in the battle prior to the duplicate unit appearing? Any other mods you've installed in the past?

We are testing out some higher morale damage changes as well as systems to increase morale while flanked by nearby friendly units and reduce it when nearby friendly units are fleeing. Will be a while before anything is ready though.
Potentially also looking at higher experience gain with a much higher cost of veterans.

This config is really more for ease of testing. It does control the numbers of units that can deploy in each battle but it's a bit of a mess behind the scenes for various technical reasons. A lot of smaller deployment numbers are hard coded so not all battles will show changes.
killsPerEffectivity = number of kills to gain 1 point of the Effectiveness stat. The others use the same format. Reducing the numbers will result in units leveling faster. Officers level based on stats gained by their units so this will affect them as a by product.

Base game value is 5. I've never tried decimals, unsure if they would work.
There is not, this is stored in the assets file. Midway through having mostly colonels is about right for the mod's intended balance. This will vary a bit depending on difficulty(more men to kill to gain xp) and player ability to kill everything available. The closest you can get is changing the xp gain which will have the side effect of increasing officer xp gain.
unitModifiers.csv
modded values:
killsPerEffectivity,350
killsPerMelee,125
movePerStamina,1700
shootPerFirearms,700
timePerMorale,4000
base game values:
killsPerEffectivity, 150
killsPerMelee, 25
movePerStamina, 1000
shootPerFirearms, 5
timePerMorale, 1800

Probably, depending on what the last version that you played was. We reduced the base game speed a while back so the default speed is a little less than half as fast as the base game. A lot of the speed perks got reduced as well. Making frequent use of the fast forward and double fast forward buttons helps until you get more used to it.
The gamespeed can also be changed in the configuration files Mod/Rebalance/ConfigFile if you try it out and don't care for it.

I think holding the fort can still work sometimes, but it feels far less consistent and I usually make it to camp in worse shape even if it does work. Going back to the base version of this battle after getting used to the larger unit sizes available in the Rebalance mod was really rough. Being outnumbered 2:1 is much easier to deal with when your units don't start with 600 men.

I still think it might be possible to corral the entire eastern reinforcements into a corner as well. I think more infantry would be needed though, the timing is just to tight to get up to the top edge and then back down to the middle. Definitely way more fun than just waiting out the timer though.

Ambush Convoy: Tips on shifting officers around to maximize their benefits, minor stat optimizations with recruits, and explanation of officer experience gain. Hopefully shown at a more reasonable speed.
Losses: 1138(991 of own units) Kills: 7195
Went very aggressive to try and take advantage of the passive AI. Only a partial success, killed all of the northern reinforcements but was unable to wrap up the eastern reinforcements and most of them escaped. Brief discussion of AI routing logic though I need to cover this in more detail at a later point.
Stay Alert: Short camp discussion of bonus reinforcement feature and some more officer swapping.
Battle is a bit of a mess, but still goes fairly well. Start with a skirmisher screen to block out the enemy cavalry and trap it in the corner, which promptly falls apart when the ghost cavalry bug strikes multiple times.
Losses: 2490 Kills: 9252

The closest I think I could get would involve copying the corps commander and renaming him. Same with the supply wagons. Would have to think about possible side effects and benefits to doing anything like that though. Adding new elements into the UI is beyond me at the moment.
I might be able to change the message text to indicate it was a division commander. Likely issue is how many characters are displayable, will look into it.
Division commanders gain xp based on a percentage of all of the units they command. So if you put them in charge of several units likely to do very well you can speed it up a bit. Honestly in the mod I largely ignore them though, it's worth more to have the better officers doing other things until fairly late in the campaign.
I have a long term project to try and make all officers a little more interesting, but my last attempt failed rather spectacularly so it's on hold at the moment. Will see if I ever get it working.